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Suppressed catalytic activity of base excision repair enzymes on rotationally positioned uracil in nucleosomes.

The majority of DNA in eukaryotic cells exists in the highly condensed structural hierarchy of chromatin, which presents a challenge to DNA repair enzymes in that recognition, incision, and restoration of the original sequence at most sites must take place within these structural constraints. To test base excision repair (BER) activities on chromatin substrates, an in vitro system was developed that uses human uracil DNA glycosylase (UDG), apyrimidinic/apurinic endonuclease (APE), and DNA polymerase beta (pol beta) on homogeneously damaged, rotationally positioned DNA in nucleosomes. We find that UDG and APE carry out their combined catalytic activities with reduced efficiency on nucleosome substrates ( approximately 10% of that on naked DNA). Furthermore, these enzymes distinguish between two different rotational settings of the lesion on the histone surface, showing a 2- to 3-fold difference in activity between uracil facing "toward" and "away from" the histones. However, UDG and APE will digest such substrates to completion in a concentration-dependent manner. Conversely, the synthesis activity of pol beta is inhibited completely by nucleosome substrates and is independent of enzyme concentration. These results suggest that the first two steps of BER, UDG and APE, may occur "unassisted" in chromatin, whereas downstream factors in this pathway (i.e., pol beta) may require nucleosome remodeling for efficient DNA BER in at least some regions of chromatin in eukaryotic cells.

Carbon-Oxygen Lyases↗

Distinctive compartmental organization of human primary visual cortex.

In the primary visual area of macaques and other monkeys, layer 4A is a mosaic of separate tissue compartments related to the parvocellular (P) and magnocellular (M) layers of the lateral geniculate nucleus. This mosaic resembles a honeycomb, with thin walls that receive direct P inputs and cores consisting of columns of dendrites and cell bodies ascending from layer 4B, a layer that receives indirect M inputs. To determine whether apes and humans have a macaque-like layer 4A, we examined the primary visual area in humans, chimpanzees, an orangutan, Old World monkeys, and New World monkeys. Apes and humans lacked the dense band of cytochrome oxidase staining in layer 4A that marks the stratum of P-geniculate afferents in monkeys. Furthermore, humans displayed a unique arrangement of presumed M-related cells and dendrites in layer 4A, as revealed with antibodies against nonphosphorylated neurofilaments and microtubule-associated protein 2. Human 4A contained a large amount of M-like tissue distributed in a complex, mesh-like pattern rather than in simple vertical arrays as in other anthropoid primates. Our results suggest that (i) the direct P-geniculate projection to layer 4A was reduced early in the evolution of the ape-human group, (ii) the M component of layer 4A was subsequently modified (and possibly enhanced) in the human lineage, and (iii) the honeycomb model does not adequately characterize human layer 4A. This is the first demonstration of a difference in the cortical architecture of humans and apes, the animals most closely related to humans.

Aged↗

Reactivity of human apurinic/apyrimidinic endonuclease and Escherichia coli exonuclease III with bistranded abasic sites in DNA.

Several oxidative DNA-damaging agents, including ionizing radiation, can generate multiply damaged sites in DNA. Among the postulated lesions are those with abasic sites located in close proximity on opposite strands. The repair of an abasic site requires strand scission by a repair endonuclease such as human apurinic/apyrimidinic endonuclease (Ape) or exonuclease III in Escherichia coli. Therefore, a potential consequence of the "repair" of bistranded abasic sites is the formation of double-strand breaks. To test this possibility and to investigate the influence of the relative distance between the two abasic sites and their orientation to each other, we prepared a series of oligonucleotide duplexes containing abasic sites at defined positions either directly opposite each other or separated by 1, 3, or 5 base pairs in the 5'- or 3'-direction. Analysis following Ape and exonuclease III treatment of these substrates indicated a variety of responses. In general, cleavage at abasic sites was slower in duplexes with paired lesions than in control duplexes with single lesions. Double-strand breaks were, however, readily generated in duplexes with abasic sites positioned 3' to each other. With the duplex containing abasic sites set 1 base pair apart, 5' to each other, both Ape and exonuclease III slowly cleaved the abasic site on one strand only and were unable to incise the other strand. With the duplex containing abasic sites set 3 base pairs apart, 5' to each other, Ape protein was unable to cleave either strand. These data suggest that closely positioned abasic sites could have several deleterious consequences in the cell. In addition, this approach has allowed us to map bases that make significant contact with the enzymes when acting on an abasic site on the opposite strand.

Binding Sites↗

Differential regulation of MDR1 transcription by the p53 family members. Role of the DNA binding domain.

Although the p53 family members share a similar structure and function, it has become clear that they differ with respect to their role in development and tumor progression. Because of the high degree of homology in their DNA binding domains (DBDs), it is not surprising that both p63 and p73 activate the majority of p53 target genes. However, recent studies have revealed some differences in a subset of the target genes affected, and the mechanism underlying this diversity has only recently come under investigation. Our laboratory has demonstrated previously that p53 represses transcription of the P-glycoprotein-encoding MDR1 gene via direct DNA binding through a novel p53 DNA-binding site (the HT site). By transient transfection analyses, we now show that p63 and p73 activate rather than repress MDR1 transcription, and they do so through an upstream promoter element (the alternative p63/p73 element (APE)) independent of the HT site. This activation is dependent on an intact DNA binding domain, because mutations within the p63DBD or p73DBD are sufficient to prevent APE-mediated activation. However, neither p63 nor p73 directly interact with the APE, suggesting an indirect mechanism of activation through this site. Most interestingly, when the p53DBD is replaced by the p63DBD, p53 is converted from a repressor working through the HT site to an activator working through the APE. Taken together, these data indicate that, despite considerable homology, the DBD of the p53 family members have unique properties and can differentially regulate gene targeting and transcriptional output by both DNA binding-dependent and -independent mechanisms.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

Maintenance of self-imposed delay of gratification by four chimpanzees (Pan troglodytes) and an orangutan (Pongo pygmaeus).

Delay maintenance, which is the continuance over time of the choice to forgo an immediate, less preferred reward for a future, more preferred reward, was examined in 4 chimpanzees (Pan troglodytes) and 1 orangutan (Pongo pygmaeus). In the 1st experiment, the apes were presented with 20 chocolate pieces that were placed, one at a time, into a bowl that was within their reach. The apes could consume the available chocolate pieces at any time during a trial, but no additional pieces would be given. The total length of time taken to place the 20 items into the bowl ranged from 60 s to 180 s. All 5 apes delayed gratification on a majority of trials until all 20 chocolate pieces were presented. Unlike in most experiments with human children using this test situation, attention by the apes to the reward was not detrimental to delay maintenance. In a 2nd experiment with the chimpanzees only, 4 foods of differing incentive value were presented in different trials in the same manner as in Experiment 1. The chimpanzees were highly successful in obtaining all food pieces, and there was no difference in performance as a function of food type.

Animals↗

Evidence of left ventricular dyssynchrony resulting from right ventricular pacing in patients with severely depressed left ventricular ejection fraction.

AIMS: Cardiac resynchronization therapy (CRT) has recently emerged as an effective treatment for patients with moderate-to-severe systolic heart failure and left bundle branch block (LBBB). Right ventricular pacing (RVP) leads to an LBBB-like pattern in the electrocardiogram. The aim of this study was to evaluate the frequency of ventricular mechanical dyssynchrony in patients induced by RVP. METHODS AND RESULTS: The study included 33 patients with a conventional single or dual chamber pacemaker, 18 with ejection fraction (EF) > 35% and 15 with EF < or = 35%. In all patients, an intrinsic rhythm without intraventricular conduction delay (QRS < or = 120 ms) was present without RVP. Two-dimensional and Doppler echocardiographic criteria for mechanical dyssynchrony [aortic pre-ejection delay (APE), interventricular mechanical delay (IVMD), delayed activation of the posterior left ventricular wall (PD), septal-to-posterior wall motion delay (SPWMD)] were evaluated in all patients with and without RVP. QRS duration showed no difference between the two EF-groups without RVP (93 +/- 10 vs. 96 +/- 9 ms), but was significantly longer in patients with low EF with RVP (152 +/- 18 vs. 181 +/- 18 ms; P < 0.001). In patients with EF > 35%, only APE was slightly prolonged by RVP (111 +/- 20 vs. 129 +/- 17 ms; P = 0.03), whereas in patients with EF < or = 35% marked pathological differences in APE (118 +/- 29 vs. 169 +/- 24 ms; P < 0.001), IVMD (22 +/- 17 vs. 58 +/- 14 ms; P < 0.001), SPWMD (103 +/- 28 vs. 125 +/- 29 ms; P = 0.004), and PD (-21 +/- 25 vs. - 39 +/- 25 ms; P = 0.005) were found. A significant correlation between QRS duration and mechanical ventricular dyssynchrony was only found for two echocardiographic parameters (IVMD, APE) with RVP. CONCLUSION: In patients with a conventional pacemaker, mechanical dyssynchrony with RVP was shown exceptionally in patients with preserved or moderately depressed systolic left ventricular (LV) function, but in nearly all patients with severely depressed systolic LV function. These patients might benefit from CRT when frequent RVP is required.

Aged↗

Hominoid dietary evolution.

During the later Palaeocene and early Miocene, catarrhine primates and the evolving hominoids had adaptations for frugivorous diets, with the emphasis on soft foods. Early in the middle Miocene the hominoids underwent a major shift, both in morphology and in habitat, with the morphology characterized by thickened enamel on the molars, enlarged incisors and massive jaws. The diet indicated by this morphology is interpreted as still mainly frugivorous but with changed emphasis, possibly towards harder objects. The thick-enamelled hominoids are found associated with more open forest habitats, and the distribution of food resources in equivalent habitats today is discontinuous both in time and in space, leading to evolutionary pressures particularly affecting locomotion, brain size and social behaviour. The earliest known hominid fossils differed little in dental and mandibular morphology from the middle Miocene apes, and the implied dietary similarity, together with ape-like patterns of dental development and retained arboreal adaptations of the postcrania, suggests little change in the foraging strategies of the earliest hominids compared with their ape ancestors and further suggests similarity in evolutionary grade. This similarity may have extended to other aspects of behaviour, for example to patterns of tool making and use, which may have been similar in the common ancestor of apes and humans to the pattern shared by the earliest australopithecines and chimpanzees.

Animals↗

An extraordinary retrotransposon family encoding dual endonucleases.

Retrotransposons commonly encode a reverse transcriptase (RT), but other functional domains are variable. The acquisition of new domains is the dominant evolutionary force that brings structural variety to retrotransposons. Non-long-terminal-repeat (non-LTR) retrotransposons are classified into two groups by their structure. Early branched non-LTR retrotransposons encode a restriction-like endonuclease (RLE), and recently branched non-LTR retrotransposons encode an apurinic/apyrimidinic endonuclease-like endonuclease (APE). In this study, we report a novel non-LTR retrotransposon family Dualen, identified from the Chlamydomonas reinhardtii genome. Dualen encodes two endonucleases, RLE and APE, with RT, ribonuclease H, and cysteine protease. Phylogenetic analyses of the RT domains revealed that Dualen is positioned at the midpoint between the early-branched and the recently branched groups. In the APE tree, Dualen was branched earlier than the I group and the Jockey group. The ribonuclease H domains among the Dualen family and other non-LTR retrotransposons are monophyletic. Phylogenies of three domains revealed the monophyly of the Dualen family members. The domain structure and the phylogeny of each domain imply that Dualen is a retrotransposon conserving the domain structure just after the acquisition of APE. From these observations, we discuss the evolution of domain structure of non-LTR retrotransposons.

Amino Acid Sequence↗

Morbidity, mortality and survival following resection for carcinoma of the rectum at Concord Hospital.

Colorectal cancer is the most common internal malignancy in Australia, and the rectum is the most common site. The morbidity, mortality and survival of 561 consecutive patients with rectal cancer who had a resection at Concord Hospital during the 16-year period 1971-86 were evaluated. More than half of the operations performed were low anterior resections (LAR), with total abdominoperineal excisions (APE) of the rectum comprising another third. There was a 5.1% mortality rate in LAR patients and a 3.1% mortality rate in the APE group. Respiratory complications, urinary tract infections and wound infections were the most common causes of morbidity in both LAR and APE. The median survival for patients treated by LAR and APE standardized for clinicopathological staging was 111.5 and 47.1 months (A), 79.0 and 65.5 months (B), 41.3 and 28.5 (C), and 14.7 and 12.4 (D), respectively.

Adult↗

Rapid improvement of acute pulmonary edema with sublingual captopril.

OBJECTIVE: To test the hypothesis that sublingual captopril produces a more rapid improvement of acute pulmonary edema (APE) than does placebo, when added to a standard regimen of O2, nitrates, morphine, and furosemide. METHODS: Prospective, randomized, double-blind, placebo-controlled clinical trial in an urban teaching hospital ED. Adults brought to the ED with APE were given captopril or placebo sublingually. Every 5 minutes a clinical APE distress score (APEX) was obtained. RESULTS: Over the first 40 minutes of treatment, the mean APEXs were significantly better for the patients given captopril [p < 0.001, F = 14.5, one-way (repeated-measures) analysis of variance (ANOVA)]. At 30 minutes, the patients given captopril had a mean APEX improvement of 43% (i.e., to 57% of initial distress); the group given the current standard regimen plus placebo improved only 25% (i.e., to 75% of initial distress; p = 0.03, multiway ANOVA). In addition, there was less respiratory failure necessitating mechanical ventilation in the captopril patients (9%) vs the placebo patients (20%), which did not achieve significance (p = 0.10, Fisher's exact test). CONCLUSION: In APE, the addition of sublingual captopril to the standard regimen of O2, nitrates, morphine, and furosemide produces more rapid clinical improvement than does the standard regimen alone.

Acute Disease↗

Indoor air pollution by alkylphenols in Tokyo.

UNLABELLED: The purposes of this study were to develop an analytical method for airborne alkylphenols (APs) using the gas chromatography/mass spectrometry (GC/MS)-SIM method and to investigate airborne C4-C9 APs pollution in houses, offices, and outdoor points in Tokyo. In addition, to identify APs emission sources in a newly built house, migration tests of APs from interior surfaces to solid extraction disks were performed. Air samples were collected from houses, offices, and outdoor points. The recovery of APs from air samples was increased by addition of ascorbic acid to the filters. 4-tert-butylphenol (4-t-BP), 4-tert-octylphenol (4-t-OP), and 4-nonylphenol (4-NP) were detected in both indoor and outdoor air. Their concentrations and detection frequencies were higher in indoor air than outdoor air. The maximum levels of 4-t-BP, 4-t-OP, and 4-NP in indoor were 387, 45.7, and 680 ng/m(3), respectively. 4-t-BP and 4-NP were detected with high frequencies (more than 97%) in indoor air samples. The concentrations of 4-t-BP, 4-t-OP, and 4-NP in indoor air were significantly correlated with room temperature (P < 0.01), and tended to be higher in newly built houses. The migration rates of APs from the floor, wall, and ceiling in the newly built house were higher in polyvinyl chloride coverings than in other materials. Practical Implications Alkylphenol ethoxylate (APE) are widely used surfactants in both industrial and domestic detergents. When these detergents are released into the environment, APE are biodegraded to the smaller chain ethoxylates and alkylphenols (APs). There are many reports about APs in aquatic environments because of their estrogenic effect on wildlife. In building materials, APs are used as antioxidant for polymer resins such as wall or floor coverings. Although APs has a lower vapor pressure, these agents are released into indoor air from the surface of polymer resins. This study surveyed concentrations of airborne AP in indoor air and outdoor air in Tokyo. In addition, to identify APs emission sources in a newly built house, migration tests of APs from interior surfaces to solid extraction disks were performed. PRACTICAL IMPLICATIONS: Alkylphenol ethoxylate (APE) are widely used surfactants in both industrial and domestic detergents. When these detergents are released into the environment, APE are biodegraded to the smaller chain ethoxylates and alkylphenols (APs). There are many reports about APs in aquatic environments because of their estrogenic effect on wildlife. In building materials, APs are used as antioxidant for polymer resins such as wall or floor coverings. Although APs has a lower vapor pressure, these agents are released into indoor air from the surface of polymer resins. This study surveyed concentrations of airborne AP in indoor air and outdoor air in Tokyo. In addition, to identify APs emission sources in a newly built house, migration tests of APs from interior surfaces to solid extraction disks were performed.

Air Pollution, Indoor↗

Immunological time scale for hominid evolution.

Several workers have observed that there is an extremely close immunological resemblance between the serum albumins of apes and man. Our studies with the quantitative micro-complement fixation method confirm this observation. To explain the closeness of the resemblance, previous workers suggested that there has been a slowing down of albumin evolution since the time of divergence of apes and man. Recent evidence, however, indicates that the albumin molecule has evolved at a steady rate. Hence, we suggest that apes and man have a more recent common ancestry than is usually supposed. Our calculations lead to the suggestion that, if man and Old World monkeys last shared a common ancestor 30 million years ago, then man and African apes shared a common ancestor 5 million years ago, that is, in the Pliocene era.

Animals↗

HMG2 interacts with the nucleosome assembly protein SET and is a target of the cytotoxic T-lymphocyte protease granzyme A.

The cytotoxic T-lymphocyte protease granzyme A induces caspase-independent cell death in which DNA single-stranded nicking is observed instead of oligonucleosomal fragmentation. A 270- to 420-kDa endoplasmic reticulum-associated complex (SET complex) containing the nucleosome assembly protein SET, the tumor suppressor pp32, and the base excision repair enzyme APE can induce single-stranded DNA damage in isolated nuclei in a granzyme A-dependent manner. The normal functions of the SET complex are unknown, but the functions of its components suggest that it is involved in activating transcription and DNA repair. We now find that the SET complex contains DNA binding and bending activities mediated by the chromatin-associated protein HMG2. HMG2 facilitates assembly of nucleoprotein higher-order structures by bending and looping DNA or by stabilizing underwound DNA. HMG2 is in the SET complex and coprecipitates with SET. By confocal microscopy, it is observed that cytoplasmic HMG2 colocalizes with SET in association with the endoplasmic reticulum, but most nuclear HMG2 is unassociated with SET. This physical association suggests that HMG2 may facilitate the nucleosome assembly, transcriptional activation, and DNA repair functions of SET and/or APE. HMG2, like SET and APE, is a physiologically relevant granzyme A substrate in targeted cells. HMG1, however, is not a substrate. Granzyme A cleavage after Lys65 in the midst of HMG box A destroys HMG2-mediated DNA binding and bending functions. Granzyme A cleavage and functional disruption of key nuclear substrates, including HMG2, SET, APE, lamins, and histones, are likely to cripple the cellular repair response to promote cell death in this novel caspase-independent death pathway.

Amino Acid Sequence↗

Modulation and roles of the endothelins in the pathophysiology of pulmonary embolism.

Recent research on the endothelins (ETs) and their pathways in acute pulmonary embolism (APE) has led to significant advances in the understanding of this disease. ETs are potent vasoconstrictors and bronchoconstrictors found abundantly in the lung and can be released by stimuli such as endothelial injury, hypoxia, or thrombin, a key product in the coagulation cascade. Many studies using different approaches and methods of inducing pulmonary embolization, both in vitro and in vivo in various species, have mostly shown that ETs play an important role in the pathophysiology of APE. These results were obtained by comparing the hemodynamic data in the presence or absence of various ETs inhibitors, but also by assessing the modulation of the ET-related elements of this system by molecular, cell biology, and pharmacological methods. Based on the current understanding, a mechanism involving the ET pathway in the pathophysiology of APE is proposed for the reader's considerations. We postulate that ETs are primary mediators in APE based on the following: (i) their source from pulmonary endothelial cells where the primary injury takes place; (ii) their direct vasconstrictive, bronchoconstrictive, and promitogenic effects via distinct ET receptors; and (iii) their indirect effects associated with the secondary release of thromboxane and other mediators, which are released from inflammatory cells and platelets, which together can potentiate the overall hemodynamic response, most specifically the pulmonary vascular bed. Such combined effects of ETs on bronchomotor and vasomotor tone in the lung can adversely affect ventilation perfusion matching and lead to severe hypoxemia without causing significant changes in the chest X-ray of these patients. Thus, we may consider ET inhibitors as future current therapeutic agents in patients with PE.

Animals↗

Rapid and accurate 13CO2 isotopic measurement in whole blood: comparison with expired gas.

Determination of 13CO2 enrichment on the CO2 released from blood by acid has been used in situations in which breath sampling is difficult. This method can be improved by measuring this enrichment on the CO2 spontaneously released from blood. Therefore, simultaneous comparisons of 13CO2 content between breath and arterialized blood added with or without acid were performed in 51 samples from human studies, using the statistical method of Bland and Altman (J. M. Bland and D. G. Altman. Lancet 1: 307-310, 1986). Strong relationships exist between the methods (r > 0.99) expressed in atom percent excess (APE). Compared with breath, the acid method overestimates the 13CO2 enrichment (0.318 +/- 0.632 APE x 1,000, P < 0.001). The acid-free method shows similar enrichments to breath (0. 003 +/- 0.522 APE x 1,000, P = 0.97) with good precision and degree of agreement (95% confidence interval 0.15 APE x 1,000). The analysis can be performed up to 5 days after sampling with a good reproducibility. In conclusion, measuring 13CO2 enrichments on the CO2 spontaneously released from blood is feasible, gives identical results to the breath method, and lessens operator manipulations. It allows study of situations in which the breath sampling method is not feasible.

Adult↗

Sylvian fissure asymmetries in nonhuman primates revisited: a comparative mri study.

Magnetic resonance images (MRI) were collected in a sample of 28 apes, 16 Old World monkeys and 8 New World monkeys. The length of the sylvian fissure (SF) and the superior temporal sulcus (STS) was traced in each hemisphere from three regions of the cerebral cortex. These three regions were labeled according to their position on the sagittal plane as lateral, medial and insular. It was hypothesized that the length and asymmetry of these fissures would be dependent on the region of measurement and that a leftward asymmetry in the SF and STS would be more robust in the great ape sample than for the monkeys. The results indicated within the ape sample a population-level leftward asymmetry in the medial and insular regions of the SF. Within the Old and New World monkey samples, the SF was leftward in the medial region at the population level, but not at the insular region. Additionally, the Old World monkeys exhibited a population-level rightward lateral SF and a rightward lateral STS. No other families exhibited population-level asymmetries in the lateral region of the SF or in any region of the STS. These results are consistent with findings reported in apes and, to a lesser extent, monkeys. MRI has excellent potential for comparing neuroanatomy across taxonomic families that will help future investigations.

Animals↗

Relationships between cerebral indices for 'extra' cortical parts and ecological categories in anthropoids.

The relationships between cerebral indices for 'extra' cortical parts associated with advanced functions [Jerison's 'extra' neurons (Nc), Hofman's 'extra' cortical volume (Ve)] and ecology and social structure were examined for a total of 86 species of anthropoids (28 species of New World monkeys, 48 species of Old World monkeys and 10 species of apes). The species were divided into a total of 39 'congeneric groups' of species which share common ecology and social structure (in most cases, congeneric groups are synonymous with genera). Both Nc and Ve were significantly larger for polygynous congeneric groups than for monogynous congeneric groups in the case of New World monkeys. In the case of Old World monkeys, both Nc and Ve were significantly larger for terrestrial congeneric groups than for arboreal congeneric groups. In the case of apes, although complete analyses could not be performed because of the limited size of the sample for which data were available, both Nc and Ve appeared to be larger for polygynous/terrestrial apes than for monogynous/arboreal apes. These results suggest that the expansion of the cerebral cortex in anthropoids may be associated with terrestriality and polygyny.

Animals↗

A new Arican miocene gibbon-like genus, Dendropithecus (hominoidea, primates) with distinctive postcranial adaptations: its significance to origin of hylobatidae.

The small, common apes of the Miocene deposits of East Africa previously assigned to two species of one genus, Limnopithecus, have been shown to differ at the generic level in both dental and postcranial features. The prior and smaller of the two species (the genotype of Limnopithecus) somewhat resembles in dental morphology African dryopithecines of subgenus Proconsul, while the larger and later described species more nearly resembles European Pliopithecus in dental details but is strikingly different from the latter in comparable postcranial bones. A new genus, Dendropithecus, is here proposed for Limnopithecus macinnesi Clark and Leakey, 1950. Numerous associated postcranial bones and dentitions of Dendropithecus macinnesi were found in a block of red limestone by L.S.B. Leakey in 1948 on Rusinga Island, Lake Victoria, Kenya. These bones make it one of the best known Miocene apes and show clearly that it had advanced away from other Miocene apes in its higher degree of development of suspensory or arm swinging postcranial adaptations. Thus, among known Miocene ape species it has the greatest demonstrated potential to be near the line of ancestry of the modern gibbon and siamang.

Africa, Eastern↗